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GeneBe

1-30716213-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_002379.3(MATN1):c.903C>T(p.Ile301=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00132 in 1,614,152 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0068 ( 13 hom., cov: 33)
Exomes 𝑓: 0.00075 ( 11 hom. )

Consequence

MATN1
NM_002379.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.540
Variant links:
Genes affected
MATN1 (HGNC:6907): (matrilin 1) This gene encodes a member of von Willebrand factor A domain containing protein family. This family of proteins are thought to be involved in the formation of filamentous networks in the extracellular matrices of various tissues. Mutations of this gene have been associated with variety of inherited chondrodysplasias. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-30716213-G-A is Benign according to our data. Variant chr1-30716213-G-A is described in ClinVar as [Benign]. Clinvar id is 783930.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.54 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0068 (1035/152284) while in subpopulation AFR AF= 0.0227 (942/41540). AF 95% confidence interval is 0.0215. There are 13 homozygotes in gnomad4. There are 488 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 13 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MATN1NM_002379.3 linkuse as main transcriptc.903C>T p.Ile301= synonymous_variant 5/8 ENST00000373765.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MATN1ENST00000373765.5 linkuse as main transcriptc.903C>T p.Ile301= synonymous_variant 5/81 NM_002379.3 P1
MATN1ENST00000477320.1 linkuse as main transcriptn.756C>T non_coding_transcript_exon_variant 3/32

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00677
AC:
1030
AN:
152166
Hom.:
13
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0226
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00465
Gnomad ASJ
AF:
0.000864
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000118
Gnomad OTH
AF:
0.00526
GnomAD3 exomes
AF:
0.00198
AC:
499
AN:
251402
Hom.:
5
AF XY:
0.00149
AC XY:
202
AN XY:
135888
show subpopulations
Gnomad AFR exome
AF:
0.0253
Gnomad AMR exome
AF:
0.00185
Gnomad ASJ exome
AF:
0.000298
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000131
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000528
Gnomad OTH exome
AF:
0.00179
GnomAD4 exome
AF:
0.000748
AC:
1094
AN:
1461868
Hom.:
11
Cov.:
35
AF XY:
0.000644
AC XY:
468
AN XY:
727232
show subpopulations
Gnomad4 AFR exome
AF:
0.0248
Gnomad4 AMR exome
AF:
0.00212
Gnomad4 ASJ exome
AF:
0.000306
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000139
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000297
Gnomad4 OTH exome
AF:
0.00176
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00680
AC:
1035
AN:
152284
Hom.:
13
Cov.:
33
AF XY:
0.00655
AC XY:
488
AN XY:
74484
show subpopulations
Gnomad4 AFR
AF:
0.0227
Gnomad4 AMR
AF:
0.00464
Gnomad4 ASJ
AF:
0.000864
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000118
Gnomad4 OTH
AF:
0.00521
Alfa
AF:
0.000955
Hom.:
0
Bravo
AF:
0.00813
Asia WGS
AF:
0.00202
AC:
7
AN:
3478
EpiCase
AF:
0.000218
EpiControl
AF:
0.000237

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeApr 20, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.63
Cadd
Benign
1.4
Dann
Benign
0.79

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs34163530; hg19: chr1-31189060; COSMIC: COSV104685921; COSMIC: COSV104685921; API